Tom & Charles, Tom, thanks for your attention to this issue -- actually, the problem is more narrow...
Charles was (only) seeing a segfault with the read_pdbstr function and PDB file 1DT7, and indeed I have been able to reproduce this on Linux with version 0.97. However, the latest 0.98 betas seem to handle the read just fine. Much of the PDB loader code was re-engineed since 0.97 to support some new scenarios (such as PDB files containing multiple independent objects). Thus, it seems that the problem has inadvertently been fixed -- I've confirm function of the latest code on all 3 major platforms without mishap. So, unless or until anyone can reproduce this crash with the latest beta, I'm going to view this as a non-issue. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Thomas Stout > Sent: Saturday, November 20, 2004 2:31 PM > To: Charles Moad > Cc: pymol-users@lists.sourceforge.net > Subject: RE: [PyMOL] cmd.read_pdbstr segfault > > > > Ah - completely different situation....I found an > installation of v0.97 (WinXP) and 1DT7 also loads fine there > - so I guess it's not inherent to version 0.97 - at least not > the windows version.... > > -Tom > > > -----Original Message----- > From: Charles Moad [mailto:cm...@indiana.edu] > Sent: Sat 11/20/2004 8:42 AM > To: Thomas Stout > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] cmd.read_pdbstr segfault > > The application actually quits, hence the seg fault error. > This happens for quite a few files, and the only trend I saw > was file size since the smaller ones had no troubles. > > - Charlie > > On Nov 19, 2004, at 6:21 PM, Thomas Stout wrote: > > > > > version 0.98 (beta 07 and beta 17) loads PDB IS 1DT7 just > fine. It's > > a little slow, but it works! Are you sure you don't have > "auto-zoom" > > off? I turn auto-zoom off by default and as a result some entries > > (like 1DT7) load but are not visible. Clicking the "zoom" button > > brings it into the center of the graphics window..... > > > > -Tom > > > > > > -----Original Message----- > > From: pymol-users-ad...@lists.sourceforge.net > > [mailto:pymol-users-ad...@lists.sourceforge.net]on Behalf > Of Charles > > Moad > > Sent: Friday, November 19, 2004 5:18 AM > > To: pymol-users@lists.sourceforge.net > > Subject: [PyMOL] cmd.read_pdbstr segfault > > > > > > pymol-0.97 cmd.read_pdbstr is dieing for remotely > large pdb files. > > One > > for example is 1DT7. I don't get a descriptive error: > > > > /usr/local/bin/pymol: line 2: 10486 Segmentation fault > /usr/bin/python > > /usr/local/lib/python2.3/site-packages/pymol/__init__.py > > $* > > > > Thanks, > > Charlie > > > > > > > > ------------------------------------------------------- > > This SF.Net email is sponsored by: InterSystems CACHE FREE OODBMS > > DOWNLOAD - A multidimensional database that combines robust > object and > > relational technologies, making it a perfect match for > Java, C++,COM, > > XML, ODBC and JDBC. www.intersystems.com/match8 > > _______________________________________________ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > ------------------------------------------------------- > > This SF.Net email is sponsored by: InterSystems CACHE FREE OODBMS > > DOWNLOAD - A multidimensional database that combines robust > object and > > relational technologies, making it a perfect match for > Java, C++,COM, > > XML, ODBC and JDBC. www.intersystems.com/match8 > > _______________________________________________ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > > >
